Make a homemade fungicide for plants:
http://www.ehow.com/how_4453670_make-garlic-fungicide-plants.html

Next, make a homemade insecticide:
http://www.ehow.com/how_2304842_make-organic-insecticide.html

Keep the bugs and insects away by planting pest repelling plants:
http://www.gomestic.com/Gardening/20-Plants-That-Repel-Pests.38427

And, finally, fix any blossom end rot you may have by:
1: Crack a few eggs, trow or cook interior. Wash eggshells thoroughly.
2: Break eggshells into little bits and pieces. Caution: may be very sharp!
3: Dig around plants to about 2 inches underground. Place eggshells and lightly work into soil.
4: Top your original soil or potting soil back over.
5: Sprinkle a little Epsom salt around the plants and make sure Ph level is 6.5 to neutral (7.0).

(Alternative or additive to blossom end rot cure):
1a: Use 1 part milk to 10 parts water to 5 parts milk to 5 parts water. Use skim or 1% fat milk. It is better to have more water than milk, as milk can sometimes cause some fungus to appear if too much is applied. I use about 2 parts milk to 9 parts water, I would estimate.

so is this fungus or lack of calcium? could I use a copper fungicide as well?

It is probably insect damage, I would guess. Try all three or four (if you want to use both blossom end rot cures; I would suggest using both) recipes/cures/preventatives I showed you. No specific order, though I would use the insecticide before using the fungicide, but like I said, it doesn't matter much which order.
You will have to repeat the insecticide and fungicide at least 3 times a week (I would suggest more) for a while.

All three ways I showed you are non-toxic.

This is what blossom end rot usually looks like on tomatoes:

You may or may not have blossom end rot, but it is good to take precautions sometimes and be one-step ahead of the game.

Thank you.. I leaning on it being blossom rot as my squash are getting it too. I will try the milk recipe as I dont eat enough eggs... Will the milk recipe work for squash as well?

With the diluted milk recipe, it is supposed to be applied as a foliage spray. I forgot to add that. Sorry! :P
How it works is that the leaves absorb many essential nutrients from the milk, just like your skin can soak up water, etc..

And yes, the diluted milk spray should work with your squash plants, too.

For more info on blossom end rot, search "Blossom End Rot" or whatever else that deals with "Blossom End Rot" on Google.com .